Data from: Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

Background. Cloud forest, characterized by a persistent, frequent or
seasonal low-level cloud cover and a fragmented distribution, is one of
the most threatened habitats especially in the Neotropics. Tree ferns are
among the most conspicuous elements in these forests and ferns are
restricted to regions in which minimum temperatures rarely drop below
freezing and rainfall is high and evenly distributed around the year.
Current phylogeographic data suggest that some of the cloud forest-adapted
species remained in situ or expanded to the lowlands during glacial cycles
and contracted allopatrically during the interglacials. Although the
observed genetic signals of population size changes of cloud
forest-adapted species including tree ferns correspond to predicted
changes by Pleistocene climate change dynamics, the observed patterns of
intraspecific lineage divergence showed temporal incongruence. Methods.
Here we combined phylogenetic analyses, ancestral area reconstruction, and
divergence time estimates with climatic and altitudinal data
(environmental space) for phenotypic traits of tree fern species to make
inferences about evolutionary processes in deep time. We used phylogenetic
Bayesian inference and geographic and altitudinal distribution of tree
ferns to investigate the ancestral area and elevation and environmental
preferences of Mesoamerican tree ferns. The phylogeny was then used to
estimate divergence times and ask whether the ancestral area and elevation
and environmental shifts were linked to climatic events and historical
climatic preferences. Results. Bayesian trees retrieved Cyathea,
Alsophila, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits
for species in these genera found in the Mesoamerican cloud forests are
recent, from the Neogene to the Quaternary. Australia was identified as
the ancestral area for the clades of these genera, except for Gymnosphaera
that was Mesoamerica. Climate tolerance was not divergent from
hypothesized ancestors for the four most significant variables or
elevation. For elevational shifts we found repeated changes from low to
high elevations. Conclusions. Our data suggest that representatives of
Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud
forests in different times and have persisted in these environmentally
unstable areas but extant species diverged recently from their ancestors.

背景
云雾林（Cloud Forest）以持续、频繁或季节性的低层云覆盖为核心特征，且分布呈碎片化格局，是受威胁程度最高的生境类型之一，尤其在新热带区（Neotropics）内。树蕨（Tree Ferns）是这类森林中最醒目的组成类群，而蕨类植物通常仅分布于最低气温极少低于冰点、全年降水充沛且分布均匀的区域。现有系统地理学数据（phylogeographic data）显示，部分适应云雾林的物种在冰期循环中可原地留存或向低地扩张，而在间冰期则发生异域性种群收缩。尽管已观测到的、包括树蕨在内的适应云雾林物种的种群数量变化遗传信号，与更新世气候变化动态的预测结果高度吻合，但种内谱系分化的模式却呈现出时间上的不一致性。

方法
本研究结合系统发育分析、祖先区域重建与分化时间估算方法，同时整合树蕨物种表型性状的气候与海拔数据（环境维度），以推演深时演化过程。我们采用贝叶斯系统发育推断手段，结合树蕨的地理与海拔分布数据，探究中美洲树蕨的祖先区域、海拔偏好与环境偏好。随后基于构建的系统发育树估算分化时间，并验证祖先区域、海拔及环境的转变是否与气候事件及历史气候偏好存在关联。

结果
贝叶斯系统发育树显示，笔筒树属（Cyathea）、桫椤属（Alsophila）、黑桫椤属（Gymnosphaera）与白桫椤属（Sphaeropteris）均形成单系支。分布于中美洲云雾林的上述各属物种的分化事件较为晚近，发生于新近纪至第四纪时期。除黑桫椤属的祖先区域被推断为中美洲外，其余三个属的类群祖先区域均为澳大利亚。针对四项最重要的环境变量与海拔梯度，各物种的气候耐受性并未与推测的祖先类群产生显著分化。在海拔迁移模式方面，我们观测到反复发生的从低海拔向高海拔的转变。

结论
本研究数据表明，桫椤科（Cyatheaceae）主要演化支的类群曾在不同时期从澳大利亚迁移至中美洲云雾林，并长期存续于这些环境不稳定的区域；而现生物种与其祖先类群的分化发生相对晚近。